Mouse Genomes Project

Adding DAS Tracks in Ensembl

To view coding SNPs in the Ensembl Genome Browser, you can add a DAS track. There is one source per strain and they are all listed in the DAS Registry, named 'MGP_[strain_name]_SNPs'.

• To add a DAS track, view a region of the mouse genome, eg. http://www.ensembl.org/Mus_musculus/Location/View?r=1:9485681-9585680, and click 'Configure this page'.
• Click the 'Custom Data' tab.
• Click 'Attach DAS'.
• Make sure 'DAS Registry' is selected in the drop down and that the other boxes are blank, then click 'Next' (and wait, though nothing seems to happen).
• Scroll down and tick the MGP_* sources you want and click 'Next' (and wait).
• Now click on the 'Main Panel' tab and the new sources you added should be listed in the 'User attached data' area. You may find that these all have labels forced on; in which case click to the left-most icon next to the source name and change it to 'No Labels' or 'Normal'.
• Now 'Save and close' and the tracks will load.

Enquiries

For further information, please contact mousegenomes@sanger.ac.uk

Related links

• Mouse Genomes Project
• Mouse Genomes Project FTP site
• Read Alignments (LookSeq)
• SNP and Indel Query
• Data Release Policy
• Mouse HapMap Imputed Genotype Resource (external site)

Latest News

• 2013-04-16 New Variants Pages
  We have launched a new interface for querying all of the sequence variants. It has been updated to include the latest variant release on GRCm38.
• 2013-03-20 GRCm38 Release
  A new release of the BAM files, SNPs/indels, and structural variants has been made on the latest mouse reference genome (GRCm38). Please see the README files in the folders for more details. Our variant querying web page will be updated to the new release in the coming weeks.
• 2013-02-27 Denovo Assemblies
  Preliminary scaffolds from SGA de novo assembly of 16 strains. Fasta files are in REL-1302-Assembly.These are scaffolds only and have not yet been organised into chromosomes.
• 2013-02-12 New SV Release
  A new release of the structural variant calls has been made on our ftp site. This release incorporates the structural variation genotypes for the FVB/NJ strain. Also, we have updated the last SNP/indel release with a minor change to the VCF to fix the annotations for multi-allelic sites (the sites/genotypes are unchanged).
• 2012-12-04 New SNP/indel Release
  A new release of the SNPs and indels for 16 of the mouse strains has been produced using the new higher quality sequencing data. The VCF files are available from the ftp site and the website query pages will be updated in the coming weeks. A new submission to dbSNP is also being prepared.
• 2012-10-16 New Sequencing Data
  New higher quality sequencing data (100bp, ~40x, HiSeq platform) is available for 16 of the strains. This has been uploaded to the ftp site. New variant calls will be posted soon.
• 2012-08-03 New Sequence Data
  New higher quality sequencing data (100bp, ~40x, HiSeq platform) is available on our ftp site for several of the strains - the rest will be posted soon.
• 2012-06-12 FVB Variant Calls
  We have posted the full set of FVB variant calls (SNPs, short indels, and structural variants) on our ftp site in VCF format. The query pages on this site will be updated in the near future to incoroporate these calls.
• 2011-11-17 FVB Strain Sequenced
  We have completed sequencing of the FVB/NJ strain to 53x sequence coverage. SNP, indel, and structural variation calls will be posted soon. The raw data is available for download from our ftp site and can browsed in LookSeq.
• 2011-09-15 Nature Publications
  We are delighted to announce that two papers have been published in Nature describing the variation found and its impact on mouse phenotypes and traits. Further details.
• 2011-08-05 Structural Variation Calls
  The entire set of structural variation calls across the 17 strains have been posted on our ftp site in the current_svs directory. These have also been submitted to DGVa under accession estd118.
• 2011-06-30 Whole-brain RNA-seq BAMs
  We have just posted the BAM files and top-hat expression values for the whole-brain RNA-Seq data on our ftp site in the current_rna_bams directory. Note this data is also available from the ENA under accession ERP000614
• 2011-06-27 Multi-tissue RNA-Seq
  We have recently completed RNA-Seq from a cross of C57BL/6J and DBA/2J across 6 different tissues and this data is available from the ENA under accession ERP000591
• 2011-06-24 Whole-brain RNA-Seq
  We have recently completed sequencing whole-brain RNA from 15 of the strains using the Illumina RNA-Seq protocol. The data has been accessioned at the ENA under ERP000614.
• 2011-06-24 Long Fragment end Sequencing
  We have recently completed sequencing the ends of 3kb fragments on the illumina platform across the mouse strains. The data is available from the ENA under study accession ERP000255
• 2011-06-23 Variant Release & dbSNP
  We have made the final release of the SNP and short indel variants. The only change from the previous release (REL-1101) is that we have filtered out chrY calls. These SNPs and indels have been submitted to dbSNP as the final published set. The SNPs and short indels are available from our ftp site. The BAM alignment files have not been changed.
• 2011-06-22 Accession Numbers
  The raw data has all been submitted to the ENA and the accession numbers and links are listed with the strain names.
• 2010-07-27 Variant Releases
  The variant calls have been steadily updated over the past few months. The Data Release section below has links to all of the latest sets of SNP and short indel calls and the online browser has also been updated to reflect the new callsets. The BAM alignment files have not been changed.
• 2010-01-13 New release
  The new release data have been loaded and are visible in the SNP query and LookSeq pages. 14 of the 17 strains are over 20x coverage (three over 30x) with the others (129S5, NZO, and WSB) all over 15x.
• 2009-12-11 New Sequencing Data
  We have made a new freeze of the sequencing data with almost all of the strains sequenced to over 20x depth. This new data has now been loaded into the Lookseq viewer. We are preparing new SNP/indel calls and hope to have these searchable very soon.
• 2009-11-03 IMGC
  Here is the poster we presented at IMGC
• 2009-11-03 Sequencing Progress
  We now have 10 strains over 20x sequencing depth and have begun to prepare a new data release (SNP, indel, SV calls) for these strains. We'll post and update when the new data has been loaded.